Limosilactobacillus fermentum in the theoretical composition was changed to Lactobacillus fermentum
## Error in dimnames(x) <- dn :
## length of 'dimnames' [1] not equal to array extent
These are the taxa that were found in the experimental data
## species taxid superkingdom phylum
## 1 Bacillus subtilis 1423 Bacteria Firmicutes
## 2 Enterococcus faecalis 1351 Bacteria Firmicutes
## 3 Escherichia coli 562 Bacteria Proteobacteria
## 4 Limosilactobacillus fermentum 1613 Bacteria Firmicutes
## 5 Listeria monocytogenes 1639 Bacteria Firmicutes
## 6 Pseudomonas aeruginosa 287 Bacteria Proteobacteria
## 7 Salmonella enterica 28901 Bacteria Proteobacteria
## 8 Staphylococcus aureus 1280 Bacteria Firmicutes
## class order family genus
## 1 Bacilli Bacillales Bacillaceae Bacillus
## 2 Bacilli Lactobacillales Enterococcaceae Enterococcus
## 3 Gammaproteobacteria Enterobacterales Enterobacteriaceae Escherichia
## 4 Bacilli Lactobacillales Lactobacillaceae Limosilactobacillus
## 5 Bacilli Bacillales Listeriaceae Listeria
## 6 Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas
## 7 Gammaproteobacteria Enterobacterales Enterobacteriaceae Salmonella
## 8 Bacilli Bacillales Staphylococcaceae Staphylococcus
## count Gram Stain EXP_sum
## 1 1740000 + 1696.4170
## 2 990000 + 845.0235
## 3 1010000 - 3888.5896
## 4 1840000 + 956.4267
## 5 1410000 + 696.8151
## 6 420000 - 100.1231
## 7 1040000 - 409.6689
## 8 1550000 + 792.1799
## is.significant N
## <lgcl> <int>
## 1: TRUE 3
## 2: FALSE 24
Full-model PERMANOVA: source + dna.isolation.method
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms")
## Df SumOfSqs R2 F Pr(>F)
## primer 2 0.073145 0.2651 1.0822 0.407
## Residual 6 0.202775 0.7349
## Total 8 0.275920 1.0000
## is.significant N
## <lgcl> <int>
## 1: TRUE 15
## 2: FALSE 66
Full-model PERMANOVA: source + dna.isolation.method
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms")
## Df SumOfSqs R2 F Pr(>F)
## primer 2 0.075489 0.26976 1.1082 0.409
## Residual 6 0.204348 0.73024
## Total 8 0.279837 1.00000
## is.significant N
## <lgcl> <int>
## 1: TRUE 63
## 2: FALSE 441
Full-model PERMANOVA: source + dna.isolation.method
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms")
## Df SumOfSqs R2 F Pr(>F)
## primer 2 0.076531 0.27168 1.1191 0.396
## Residual 6 0.205161 0.72832
## Total 8 0.281691 1.00000
## is.significant N
## <lgcl> <int>
## 1: FALSE 910
## 2: TRUE 165
## 3: NA 5
Full-model PERMANOVA: source + dna.isolation.method
## Permutation test for adonis under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 999
##
## adonis2(formula = otutab_t ~ primer, data = sampdat, method = distance, by = "terms")
## Df SumOfSqs R2 F Pr(>F)
## primer 2 0.077607 0.27403 1.1324 0.384
## Residual 6 0.205601 0.72597
## Total 8 0.283209 1.00000